


The Lies We Were Told

by alienbabybitch (mikeyskies)



Category: The Lone Gunmen (TV), The X-Files
Genre: Alien Biology, Alternate Universe, Alternate Universe - Canon Divergence, F/F, F/M, Faked Death, Gen, Human Experimentation, Lesbian Character, Martha's Vineyard, The Lone Gunmen - Freeform, gene manipulation
Language: English
Status: In-Progress
Published: 2018-02-12
Updated: 2018-03-14
Packaged: 2019-03-17 03:17:59
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 3
Words: 2,934
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/13650324
Author URL: https://archiveofourown.org/users/mikeyskies/pseuds/alienbabybitch
Summary: 15 years ago. It took her 15 years to find her son. Her and Mulder's son. She knew better than to question things when she wasn't sure she wanted to know the answers. She could look past the alien genetics when it came to her son- but as a scientist, she felt like she was asking the same two questions: how and why?Essentially, the Lone Gunmen faked their deaths, CGB Spender has a few secrets he's not telling, and Scully learns the answers to the questions she's not asking.





	1. Chapter 1

Jackson. His name was Jackson. Not William, not Will, Not William Fox Scully. Jackson Van de Kamp. That was his real name, the name his real parents gave him, the name his real parents called him. These people weren’t his real parents. He knew they were his biological parents. He knew they loved him. He knew they cared about him. He knew that this poor woman didn’t want to put him up for adoption. He knew she wanted to raise him, but knew she couldn’t. He didn’t blame her. He wanted to know her, know where he came from, to learn more than the glimpses in her life from the episodes and seizures. That didn’t make her his mom. His real mom was dead. She was just a stranger.

He plugged his earbud back in and leaned back in his seat on the bus. He had been living with these people he called his biological parents for nearly a month and he still wasn’t used to it. It sucked. Halfway through junior year moving from a suburb to middle of nowhere Virginia wasn’t how he wanted to spend February break. The house was nice- older than his parents’, smaller too. He still had his own room, unless you counted the geriatric Pomeranian by the name of Queequeg II who seemed to have rule of the entire house. The bus ride from the county school, however, was nearly an hour, and that’s one of many things he hated about this situation. Jackson Van de Kamp was the man you wanted to know. He was designated hitter for his school’s baseball team and a damn good one at that. He was strong, but sensitive, the type that the girls end up falling for in rom-coms. He was smart, all honors classes and three AP classes. On track to graduate a year early. Not bad looking either, not that he’d admit it. William Scully was a pity story. The long lost son of two FBI agents long past their primes.

He clutched his keys in his hand as the bus came to a screeching halt, dropping him off at the end of a long drive way. He sighed as he made his way almost half a mile to the house. He didn’t look up as he unlocked the door, effortlessly shrugging his backpack off is shoulder and into his hand to drag it up the stairs behind him. He almost kept walking until something caught his nose. He wouldn’t notice it at the school, or out in public, but the scent of cigarette smoke felt heavy in the air here. His jaw dropped as he turned to face the living room. A man, older than a man who smelled so densely of smoke alive, sat there in the chair, looking perfectly at home, cigarette dangling from his lips. Behind him stood his moth- no, not his mother. Your mother loved you. _She_ gave you away. Behind him stood Scully, gun barrel pushed against his head. Yet the look on the man’s face was one of ease.

“Why hello William,” The words oozed from the man’s mouth in a trail of smoke. “Your mother and I were just talking about you,” He sat back, resting his head against the barrel of the gun.

“My name’s not William,” The boy says through grit teeth, trying to keep a calm exterior, despite the fact that his hands were shaking with an anxiety he hadn’t felt since he found his real parents bodies sprawled across the floor. “It’s Jackson.” The old man smiled some more, leaving Jackson to wonder how the butt of the cigarette managed to stay between his lips as he spoke.

“Pleased to make your acquaintance,” he said, taking a drag of his cigarette, letting the smoke slither out in a way that gave the words a sinister connotation.

“Don’t say another word to him,” Scully warned. The man laughed.

“Cant a man have a nice conversation with his grandson nowadays? Dana, don’t tell me you too aren’t interested in how your miracle came to be.” He oozed. “I’m afraid I haven’t been entirely honest with you, now have I?” Scully scoffed.

“You’re about 18 years too late with you apologies, you son of a bitch,” she fired back. He tsked her and turned back to Jackson.

“I’m glad I get to see one of my experiments matured, and so nicely. What a handsome young man you are.” Jackson felt himself visibly shudder, filled with terror at the strange man’s words. Experiment? What the hell was he saying? “My plan was perfect. I use my own son’s genetic material along with his ‘partners’” the tone of that word was suggestive enough that it made Jackson cringe and Scully tighten her grip on the gun, “to create an embryo that was purely resistant to the alien colonization.” He sat back, smug look on his face. “Of course, only a few of the fetuses survived. And only two surviving an hour past birth. One being you, the other being the first child gestated entirely in an artificial womb.” Scully was no longer scared. In fact, she was anything but. She was angry.

“You- you son of a BITCH!” she cried out. “YOU CLONED MY CHILD? YOU USED ME TO HOST AN EXPERIMENT?” She took a deep breath in, widening her stance, cocking the gun. “Give me one good reason why I shouldn’t shoot you now.”

“Because,” he sat back, smug look on his face. “I still know things you don’t. Such as, nothing we did involved cloning. It was an entirely different child.” It was Jackson who spoke next.

“And where is that child now?” The smoking man laughed.

“If I knew, what would I be doing here?”

 

**September 24, 2003- Baltimore, Maryland**

 

                “Cut the shit Ringo, tell us what you got.”

                “I’m linking the video footage now. Frohike, don’t get your panties in a twist.” Langley leaned back in the swivel chair, overlooking the computer hooked up to the security cameras of the government building. “What are we even looking for again?”

“Both Mulder and Scully showed up on the records for this one experiment, ROS4713. We’re here to erase their names and find out why.” Byers shook his head, shining the flashlight on the door. “We’re here.”

“I’m cutting the wires to the door right now, you’ll have 4 minutes and 59 seconds to get in and out before it resets.”

                “Got it Langley,” Frohike spat into the ear piece as the door clicked and Byers kicked it open.

                “Hey Ringo, we’re going to need to do more than just a file dump here,” he chuckled nervously into the earpiece.

                “Why?! What is it?”

                “It’s a kid, Langley. A little girl.”


	2. Chapter 2

West Tisbury, Massachusetts  
6:22 A.M. March 2018

Two sharp knocks rapped on the door. “Hey Spooks? Get your ass out of bed, you’re going to be late.”

“Oh, fuck off,” mumbled the pile of blankets as the door was flung open wide. Two blue eyes poked out, hidden under blankets and furrowed brows. “It rained yesterday, the snow’s gone. I’ll bike.”

Byers rolled his eyes. “You couldn’t have told me that before I get up to wake you up?”

“Nope,” the lump of blankets shifted once again, the figure underneath emerging and propping herself up on her elbows. “Sorry, but you have to open at 7:30 anyway.” Samantha sighed, running a hand through messy auburn hair, sticking out in every direction, more like the greasy older brother from a 2000s movie than Einstein. “Do you want to let me to go back to sleep?”

“Actually, you said you wanted to go in early, to meet with your AP Lit teacher. You’re the only sophomore in that class, isn’t that important?”

She shrugged, getting out of bed and shooing him out of the room, flipping the light switch. The lamps illuminated the room, revealing an old acoustic guitar propped up against a bookcase, a half dozen baseball caps, a paper strewn desk, a few textbooks for world history and anatomy. The walls were painted white and bare, except for the Star Wars and Lazarus Bowl posters the guys got her a few years back, a couple of newspaper clippings, and few photos pinned up on a cork board. Mostly photos of her and the gunmen, or her friends, watching fireworks over the ocean, playing in the marsh, curly haired five year olds playing tee ball, and skinny 7th graders with braces at the middle school dance. Nothing special. Not what one would expect from Samantha Mulder-Scully-Byers-Langley-Fro-- well, fuck it, It was Samantha Mulder II in the system, Sammy to friends, and “Spooky” to the men who were a) not her biological parents, b)not actually her legal guardians, and c) not gay.

She tore off the purple MVRHS Softball t-shirt and grabbed an old “Alien chicks do it better- Visit Roswell” shirt Langley once bought her. After spending two or three minutes attempting to tame the mess of hair, she gave up, instead grabbing a Red Sox cap, and picked up her backpack by the door. After 5 ½ miles of biking, it was nearly 7:10, about 20 minutes until class started. She shook out her hat hair, having it flattened out slightly during the ride, and walked over to the library. “Hey dirtbag,” a boy, about her age, maybe a bit older, laughed. She smiled, crinkling her nose, freckles spreading across her face.

“Fuck off, Max,” she grinned, rolling her eyes. “At least I did the APUSH homework.”

“Speaking of which, can I copy the notes?” he pleaded, She gave him a look of disgust, and he sulked, “C’mon, we can’t all naturally be geniuses.”

She sighed, “Here, but you owe me.” she said, tossing the notebook to the side. He smirked.

“Speaking of which, have you asked Lydia to the dance yet?”

“Of course not, stupid. She has a boyfriend. And mhate to break it to you, but rural New England isn’t really the safest place to take your same sex partner to the dance,” she sighed. “Don’t you have to get to class or something?” He laughed.

“I’ll see you later man,” he sauntered away as the bell rang for the five minute warning before first period.

  
Somewhere in Virginia

Mulder ran a hand through his hair, the winding dirt roads peaceful, almost soothing in his mind as he pulled into his long driveway. To his knowledge, nothing was wrong as he opened the door to his own home.

“Scully? You home yet?” He called, only to feel his partner in his arms within seconds. He pet her hair, burying his face into her neck only to smell- “Scully, you smell like-“

“He was here Mulder,” her voice was shaky and unconfident. She was scared and her voice said what the words didn’t. “He wanted something from us.”

“What did he want?”

“I don’t know, something about a girl, whatever he wanted, it’s not here.”

“The girl, he was talking about-“ William interrupts, fingers massaging his temples as he sat back down, closing his eyes, as if it hurt him to remember what he was thinking about. “I’ve seen her before.”

“How can you tell, how do you know it’s her?”

“Because!” He practically shouts before sitting back down and quietly reminiscing. “I think she’s my sister.”


	3. Chapter 3

**Notes for the Chapter:**

> This is really bad but i dont want to fix it so enjoy

**September 26, 2007**

The room wasn’t clean, but it was a type of mess that seemed more clandestine than a hospital room. The finger paintings on the wall along with the educational posters plastered on the wall gave the appearance of a welcoming environment, despite the chills running down John Fitzgerald Byers’ spine. He glanced over at the man nervously bouncing his leg nervously next to him, stringy bleached blond hair falling in front of his face. The click of high heels caused both men to startle, as if out of a trance.

“Hello, I’m Mrs. Dotson,” smiled the woman, who sat down across from them. She was in her mid-thirties, brown hair just beginning to go grey at the roots. She wore make up, more make up than most women they knew, not that they knew that many women.

“John Byers,” he said with a tight smile across his face. He extended a hand across the table, leading Langly to do the same.

“Richard Langley.”

“Nice to meet you, you must be Samantha’s father and, well,” She nodded at Byers, eyes flitting between the two men. She cleared her throat. “I’d just like to make it clear, we respect everyone here at West Tisbury Charter school, regardless of race, gender and, well, _sexuality_.” She smiled, too sweetly for it to be genuine. Byers flushed nervously.

“We’re not together, Samantha is our god daughter,” He explained, trying to make the situation as least awkward as possible. “Her parents… they’re not here anymore. She lived with her grandfather” he’s not lying, Byers supposes, “before he… well, he’s not in the picture either.” Mrs. Dotson’s painted eyebrows soften, as Langly nodded in sympathetic agreement.

“Well, I suppose that explains some of the issues we’ve observed.” She smiled condescendingly, in a way that made Byers’ stomach churn. He swallowed hard.

“But not all of them?”

She shook her head, giving the same sickly sweet smile as before.

“Samantha seems to be exhibiting behaviors we attribute with issues at home. She talks to herself more than normal, despite going speechless when interacting with her peers. She has an overactive imagination. Whenever we share things at story time, she seems intent on scaring the other kids with these made up horror stories about these god awful experiments involving aliens. Mr. Langly?” She seemed to realize him dosing off, and called him back to attention. “Mr. Langly, what do you do for a living?”

“I’m a computer technician, Byers, our other friend and I used to work for a newspaper back before Sammy came about. Still do a few printings a year if you’re interested.”

“That’s quite alright,” she reassured them, “But you have a steady income, am I correct? You are able to provide for her?”

“Yeah. I wouldn’t consider us rich, but we have a small business fixing people’s computers and laptops. It pays the bills, and we live comfortably.” Byers explained. “I don’t think Samantha is unhappy, she just went through a lot as a little kid and she copes in a way that some kids do.”

She sighed, shoving the files back into the manila folder on the desk. She smiled sympathetically at the men, “I know shes been through a lot, but you should talk to her about this. We try to make the first few weeks of kindergarten easy and are more lenient, but if we see any further problems, we will be meeting again.”

“Of course.”

 

 

  **March 3, 2012  
**

She was 9 when she had the first episode. She was at the table working on her science fair project, a model of the solar system, talking to Jimmy and Frohike about aliens, when she stopped. She didn’t do anything, just stared out at the room around her before her eyes rolled back in her head and she collapsed into the chair. They rushed over to her, Jimmy arriving there first.

“Spooky? Spooky, can you hear me?” Jimmy ran over to her, shaking her slightly. “I think she’s dead.”

“She’s not dead, dumbass,”Frohike scoffed, before checking he vitals, trying not to panic. “Samantha? Samantha Dana Mulder? Can you hear me?”

“What’s the problem?” Byers ran into the room at the sounds of Frohike’s frantic calls.

“She’s not responding, she-“

“Where am I?” Samantha asked wearily, as if coming out of a trance. She looked around at her surroundings, blinking.

“Shh, Spooky, its okay, you’re home, with us, remember? Do you know what just happened to you?”

“They’re not coming for a while.”

“Who’s not coming, sweetheart?”

“The aliens,” She smiled, innocently. The men shared a glance.

“How do you know this?” Frohike asked the girl, who was back to work on her project. He wasn’t going to admit it, but she was almost as tall as he was now, though he insisted he was shrinking with old age.

“Mommy told me.”

“Who told you this?” Byers looked at her even more skeptically.

“My mommy,” she said, as if it wasn’t obvious the first time, “She’s really pretty and has long orange hair but its lighter than mine and dresses like a doctor. I see her sometimes. I don’t think she knows it’s me. She calls me Will sometimes.”

“How do you know it’s your mommy?”

“Grandpa told me.” Byers and Frohike shared a glance.

“Do you talk to grandpa?” Byers prayed for the answer he received.

“No, but he talked about her when I was little. I remember seeing a picture of her.” She said. They shared a nervous glance, she remembered more about her time with the smoking man than any of them had thought. 

“How about we go take a nap, okay Spooks?” Frohike tried to get her off this topic, the less she thinks about the Cigarette man, the better.

“But I’m not tired, I haven’t napped since we had to stay up late for the fireworks last summer.” She protested.

“You were just sick, you need to rest. Go with Jimmy to get some sleep.”

“Fine,” she pouted up the stairs. Jimmy following behind like a puppy, an allusion he would probably link back to Old Yeller.

“Houston” Byers said,looking over at Frohike.

“Boy,do we have a problem.”


End file.
